I am new to JMol and I want to use it to visualize results from a
Molecular Fragment Dynamics simulation. The idea is to handle the
fragments as atoms thus I have to define my own elements.
1) Is it possible to define your own elements with their own names,
colors , size(radius/volume), ... using the JMol scripting abilities.
2) I want to use the XYZ-File format to code my fragment data. May I
load several XYZ-Files in a single JMol view.
3) When I use the attached class to access a JMol panel and the
JmolSimpleViewer openStringInline method. I cant see any rendered atoms
although the output console writes that atoms have been created:
The Resolver thinks Xyz
reading 9000 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty
"auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Babel
9000 atoms created